{"id":"https://openalex.org/W2165765309","doi":"https://doi.org/10.1093/bioinformatics/btu828","title":"VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications","display_name":"VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications","publication_year":2014,"publication_date":"2014-12-17","ids":{"openalex":"https://openalex.org/W2165765309","doi":"https://doi.org/10.1093/bioinformatics/btu828","mag":"2165765309","pmid":"https://pubmed.ncbi.nlm.nih.gov/25524895"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu828","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu828","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1469/50306493/bioinformatics_31_9_1469.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1469/50306493/bioinformatics_31_9_1469.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014201647","display_name":"John C. Mu","orcid":"https://orcid.org/0000-0002-9666-8528"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John C. Mu","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005444139","display_name":"Marghoob Mohiyuddin","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marghoob Mohiyuddin","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100402604","display_name":"Jian Li","orcid":"https://orcid.org/0000-0003-3097-7210"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jian Li","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046286565","display_name":"Narges Bani Asadi","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Narges Bani Asadi","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark B. Gerstein","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078568342","display_name":"Alexej Abyzov","orcid":"https://orcid.org/0000-0001-5405-6729"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexej Abyzov","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015401462","display_name":"Wing Hung Wong","orcid":"https://orcid.org/0000-0001-7466-2339"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wing H. Wong","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058892069","display_name":"Hugo Y. K. Lam","orcid":"https://orcid.org/0000-0002-0564-6105"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hugo Y.K. Lam","raw_affiliation_strings":["1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94035, USA, 2Department of Bioinformatics, Bina Technologies, Redwood City, CA 94065, USA, 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 4Mayo Clinics, Department of Health Sciences Research, Rochester, MN 55902, USA, 5Department of Statistics, Stanford University, Stanford, CA 94035, USA and 6Department of Health Research and Policy, Stanford University, Stanford, CA 94035, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5058892069"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6762,"has_fulltext":true,"cited_by_count":96,"citation_normalized_percentile":{"value":0.83115222,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"31","issue":"9","first_page":"1469","last_page":"1471"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.629800021648407,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.629800021648407,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.22360000014305115,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.09350000321865082,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7335534691810608},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.720422625541687},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.6981494426727295},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5509577393531799},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5042213201522827},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4399440288543701},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4320392906665802},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4301875829696655},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.4187888503074646},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40820467472076416},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3822875916957855},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18569469451904297},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15906351804733276},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.14732909202575684},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13092777132987976},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.08465245366096497}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7335534691810608},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.720422625541687},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.6981494426727295},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5509577393531799},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5042213201522827},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4399440288543701},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4320392906665802},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4301875829696655},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.4187888503074646},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40820467472076416},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3822875916957855},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18569469451904297},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15906351804733276},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.14732909202575684},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13092777132987976},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.08465245366096497},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu828","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu828","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1469/50306493/bioinformatics_31_9_1469.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25524895","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25524895","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4410653","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/btu828","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu828","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu828","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1469/50306493/bioinformatics_31_9_1469.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165765309.pdf","grobid_xml":"https://content.openalex.org/works/W2165765309.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1596062789","https://openalex.org/W2065817684","https://openalex.org/W2069577154","https://openalex.org/W2095680943","https://openalex.org/W2116126626","https://openalex.org/W2118151336","https://openalex.org/W2119180969","https://openalex.org/W2134199796","https://openalex.org/W2138601221","https://openalex.org/W2147733682","https://openalex.org/W2150264767","https://openalex.org/W2150506261","https://openalex.org/W2154397429","https://openalex.org/W2155306111","https://openalex.org/W2157539385","https://openalex.org/W2166657289","https://openalex.org/W2255107171","https://openalex.org/W3098304617","https://openalex.org/W4394666350","https://openalex.org/W6635813232","https://openalex.org/W6674561012","https://openalex.org/W6677585479"],"related_works":["https://openalex.org/W2917361787","https://openalex.org/W1673677440","https://openalex.org/W2365197990","https://openalex.org/W3140604778","https://openalex.org/W3101523611","https://openalex.org/W2146245718","https://openalex.org/W3016691437","https://openalex.org/W2255506873","https://openalex.org/W2886064359","https://openalex.org/W1558071211"],"abstract_inverted_index":{"SUMMARY:":[0],"VarSim":[1,59],"is":[2,79,129,159],"a":[3,25,40,63,95,104,114],"framework":[4,84],"for":[5,135],"assessing":[6],"alignment":[7],"and":[8,35,61,74,88,113,148,157],"variant":[9],"calling":[10],"accuracy":[11],"in":[12,110,138,146],"high-throughput":[13],"genome":[14],"sequencing":[15],"through":[16],"simulation":[17],"or":[18],"real":[19],"data.":[20],"In":[21],"contrast":[22],"to":[23,52,100,106,119,153],"simulating":[24],"random":[26],"mutation":[27],"spectrum,":[28],"it":[29,128],"synthesizes":[30],"diploid":[31],"genomes":[32,56],"with":[33,123,151],"germline":[34],"somatic":[36],"mutations":[37,51],"based":[38],"on":[39],"realistic":[41],"model.":[42],"This":[43],"model":[44],"leverages":[45],"information":[46],"such":[47],"as":[48],"previously":[49],"reported":[50],"make":[53],"the":[54,130,155],"synthetic":[55],"biologically":[57],"relevant.":[58],"simulates":[60],"validates":[62],"wide":[64],"range":[65],"of":[66],"variants,":[67,71],"including":[68],"single":[69],"nucleotide":[70],"small":[72],"indels":[73],"large":[75],"structural":[76],"variants.":[77],"It":[78],"an":[80],"automated,":[81],"comprehensive":[82,132],"compute":[83],"supporting":[85],"parallel":[86],"computation":[87],"multiple":[89],"read":[90,102],"simulators.":[91],"Furthermore,":[92],"we":[93],"developed":[94],"novel":[96],"map":[97],"data":[98,167],"structure":[99],"validate":[101],"alignments,":[103],"strategy":[105],"compare":[107],"variants":[108,158],"binned":[109],"size":[111],"ranges":[112],"lightweight,":[115],"interactive,":[116],"graphical":[117],"report":[118],"visualize":[120],"validation":[121,133],"results":[122],"detailed":[124],"statistics.":[125],"Thus":[126],"far,":[127],"most":[131],"tool":[134],"secondary":[136],"analysis":[137],"next":[139],"generation":[140],"sequencing.":[141],"AVAILABILITY":[142],"AND":[143],"IMPLEMENTATION:":[144],"Code":[145],"Java":[147],"Python":[149],"along":[150],"instructions":[152],"download":[154],"reads":[156],"at":[160,170],"http://bioinform.github.io/varsim.":[161],"CONTACT:":[162],"rd@bina.com":[163],"SUPPLEMENTARY":[164],"INFORMATION:":[165],"Supplementary":[166],"are":[168],"available":[169],"Bioinformatics":[171],"online.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}